[gmx-users] Parametrisation of the heteroatomic pdb
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Nov 10 10:01:12 CET 2011
On 10/11/2011 7:36 PM, James Starlight wrote:
> Thanks Mark,
>
> 1) By the way do you know any database where I could obtain
> information about function of the specific CAP groups ?
> E.g as I know the most spread CAP on N is ACE group but in my case
> there is For ( simple COH group) instead of ACE.
>
> I think that parametrisation of such simple groups should not be very
> complicate but it's strange that I've not found already built topology
> for them.
People use acetyl rather than formyl cap either because that's what was
used in the experimental system, or because they are simulating a
fragment from a larger peptide and acetyl makes for a better model of a
peptide bond than formyl for only a small extra cost. I don't even know
that any force fields have parameters for H-C(O)-N(H)-R. I suggest you
use acetyl.
>
>
> 2) Also I've tried to made topology for D amoniacids. I've started
> with the topology of L analogs e.g for D-val I've created enty based
> on the Val in .rtp and .hdb files. Not I think I should to invert
> impropers for the Calpha atoms that new topology represent to true
> D-isomer :) But I'm not sure about how to make it correctly :)
>
> In .itp I've found for new DVA residue
>
> [ impropers ]
> ; ai aj ak al gromos type
> N -C CA H gi_1
> CA N C CB gi_2
> CA CG1 CG2 CB gi_2
> C CA +N O gi_1
>
> here there are 2 enties for the Ca atoms. What should I do with it for
> invertion?
First, identify that there's anything to invert. Look at the #define
lines for gi_1 and gi_2 and the manual sections for impropers. There's
nothing associated with any handedness. The impropers for chirality
prevent inversion, rather than enforcing a particular chirality. You can
test this yourself. Make a .tpr of an L-amino acid and .gro files of
each chirality, and then use mdrun -rerun Lconfiguration.gro -s
Lconfiguration and compare with mdrun -rerun Rconfiguration.gro -s
Lconfiguration.
Mark
>
> James
>
>
> 2011/11/10 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
>
> On 10/11/2011 7:05 PM, James Starlight wrote:
>> Justin,
>>
>>
>> I've also look for the cap editing in the pymol but it seems that
>> that function lacks in that program
>>
>> By the way, what are specificity of such Cap groups ? Do they are
>> only sheld charges on the termi or have something addition function?
>
> They can. The purpose of a simulation is to provide a model of
> reality. How one would wish to cap a peptide depends what is being
> modelled under what conditions with what objectives in mind.
>
>
>>
>> What difference beetwen different caps I cant understand why in
>> my structure there are so non-standart groups.
>
> Shrug. We don't even know what they are... Wherever you sourced
> your starting structure should discuss how and why the termini
> have such caps.
>
> Mark
>
>
>>
>>
>> James
>>
>> 2011/11/9 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>> James Starlight wrote:
>>
>> Justin,
>>
>> Could you tell me another alternative ways to replace
>> existing cap groups in my pdb besides xleap ? ( I've had
>> many problems with the pdb's processed by this soft).
>> Also I've tried to make topology for the non-standart
>> caps by PRODRG but I also have some problems with such
>> parametrisation.
>>
>>
>> Unless you describe your problems, there's very little anyone
>> can or will try to do to help you. I've never had a problem
>> with an xleap coordinate file, so I can't offer you any
>> additional guidance with that. Otherwise, there are dozens
>> of programs that are capable of drawing molecules or editing
>> files. See, for instance:
>>
>> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
>>
>> -Justin
>>
>>
>> Also I've not found suitable topology for some D-isomers
>> ( it's strange that parametriation for such typical
>> non-standart residues is absent in all force fields ). As
>> I understood I cant use topology of L-analogs for the
>> parametrisation of such D-forms because I dont know
>> suitable parameters for dihedrals for instance.
>> Have someone pre-built parameters for the D-aa for Gromos
>> or Charmm force field?
>>
>>
>> Thanks,
>>
>> James
>>
>> 2011/10/29 Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>>>
>>
>>
>>
>>
>> James Starlight wrote:
>>
>> Justin, hello!
>>
>> Could you tell me what exactly program from the
>> Amber tools
>> package you've used for the KALP peptide
>> preparation e.g for
>> capping ?
>>
>>
>> xleap
>>
>> At this point, please start a new thread for your
>> questions, as
>> these topics are completely unrelated to where you
>> started.
>>
>> -Justin
>>
>>
>> -- ==============================__==========
>>
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
>> (540) 231-9080
>> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin <http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================__==========
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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